Author: tlinnet
Date: Wed Jan 14 16:41:27 2015
New Revision: 27166
URL: http://svn.gna.org/viewcvs/relax?rev=27166&view=rev
Log:
Merged revisions 27159-27165 via svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/trunk
........
r27159 | tlinnet | 2015-01-14 14:45:17 +0100 (Wed, 14 Jan 2015) | 3 lines
Added save state for test of bug 23186.
Bug #23186 (https://gna.org/bugs/index.php?23186): Error calculation of
individual parameter "dw" from Monte-Carlo, is based on first spin.
........
r27160 | tlinnet | 2015-01-14 14:45:20 +0100 (Wed, 14 Jan 2015) | 3 lines
Added systemtest "Relax_disp.test_bug_23186_cluster_error_calc_dw", which
shows the failure of monte carlo simulations error calculations.
Bug #23186 (https://gna.org/bugs/index.php?23186): Error calculation of
individual parameter "dw" from Monte-Carlo, is based on first spin.
........
r27161 | tlinnet | 2015-01-14 14:55:37 +0100 (Wed, 14 Jan 2015) | 3 lines
Added additional test for r2a parameter.
Bug #23186 (https://gna.org/bugs/index.php?23186): Error calculation of
individual parameter "dw" from Monte-Carlo, is based on first spin.
........
r27162 | tlinnet | 2015-01-14 15:20:02 +0100 (Wed, 14 Jan 2015) | 5 lines
Attempt to implement GUI test: --gui-tests
General.test_bug_23187_residue_delete_gui
This will NOT catch the error.
bug #23187: (https://gna.org/bugs/index.php?23187): Deleting residue in
GUI, and then open spin viewer crashes relax.
........
r27163 | tlinnet | 2015-01-14 15:25:07 +0100 (Wed, 14 Jan 2015) | 3 lines
Added test for spin independet error of k_AB.
Bug #23186 (https://gna.org/bugs/index.php?23186): Error calculation of
individual parameter "dw" from Monte-Carlo, is based on first spin.
........
r27164 | bugman | 2015-01-14 15:35:01 +0100 (Wed, 14 Jan 2015) | 8 lines
Fix for the showing of the spin viewer window in the GUI tests.
The show_tree() method of the main GUI window class was not calling the
custom
self.spin_viewer.Show() method, as required to set up the observer objects
required to keep the spin
viewer window updated. The value of status.show_gui was blocking this.
Instead the show argument
of this Show() method is being set to status.show_gui to allow the method
to always be executed.
........
r27165 | tlinnet | 2015-01-14 16:10:03 +0100 (Wed, 14 Jan 2015) | 3 lines
Fix in dispersion API, to set error value for clustered values.
Bug #23186 (https://gna.org/bugs/index.php?23186): Error calculation of
individual parameter "dw" from Monte-Carlo, is based on first spin.
........
Added:
branches/nmrglue/test_suite/shared_data/dispersion/bug_23186.bz2
- copied unchanged from r27165,
trunk/test_suite/shared_data/dispersion/bug_23186.bz2
Modified:
branches/nmrglue/ (props changed)
branches/nmrglue/gui/relax_gui.py
branches/nmrglue/specific_analyses/relax_disp/api.py
branches/nmrglue/test_suite/gui_tests/general.py
branches/nmrglue/test_suite/system_tests/relax_disp.py
Propchange: branches/nmrglue/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jan 14 16:41:27 2015
@@ -1 +1 @@
-/trunk:1-27157
+/trunk:1-27165
Modified: branches/nmrglue/gui/relax_gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/gui/relax_gui.py?rev=27166&r1=27165&r2=27166&view=diff
==============================================================================
--- branches/nmrglue/gui/relax_gui.py (original)
+++ branches/nmrglue/gui/relax_gui.py Wed Jan 14 16:41:27 2015
@@ -779,8 +779,8 @@
return
# Open the window (the GUI flag check is inside the Show method).
- if status.show_gui and not self.spin_viewer.IsShown():
- self.spin_viewer.Show()
+ if not self.spin_viewer.IsShown():
+ self.spin_viewer.Show(show=status.show_gui)
def state_load(self, event=None, file_name=None):
Modified: branches/nmrglue/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/specific_analyses/relax_disp/api.py?rev=27166&r1=27165&r2=27166&view=diff
==============================================================================
--- branches/nmrglue/specific_analyses/relax_disp/api.py (original)
+++ branches/nmrglue/specific_analyses/relax_disp/api.py Wed Jan 14
16:41:27 2015
@@ -1123,8 +1123,8 @@
param_name, si, mi = param_index_to_param_info(index=index,
spins=spins)
else:
param_name = aux_params[index - total_param_num]
- si = 0
- mi = 0
+ si = None
+ mi = None
# The parameter error name.
err_name = param_name + "_err"
@@ -1140,8 +1140,15 @@
# Model and auxiliary parameters.
else:
- for spin in spins:
- setattr(spin, err_name, error)
+ # If clustered paramater:
+ if si == None:
+ for spin in spins:
+ setattr(spin, err_name, error)
+
+ # If independent value.
+ else:
+ # Set the value.
+ setattr(spins[si], err_name, error)
def set_param_values(self, param=None, value=None, index=None,
spin_id=None, error=False, force=True):
@@ -1486,7 +1493,9 @@
if model_param:
param_name, si, mi = param_index_to_param_info(index=index,
spins=spins)
if not param_name in ['r2eff', 'i0']:
- si = 0
+ if si == None:
+ si = 0
+
else:
param_name = aux_params[index - total_param_num]
si = 0
Modified: branches/nmrglue/test_suite/gui_tests/general.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/gui_tests/general.py?rev=27166&r1=27165&r2=27166&view=diff
==============================================================================
--- branches/nmrglue/test_suite/gui_tests/general.py (original)
+++ branches/nmrglue/test_suite/gui_tests/general.py Wed Jan 14 16:41:27
2015
@@ -72,6 +72,28 @@
self.assertEqual(cdp_name(), 'mf')
+ def test_bug_23187_residue_delete_gui(self):
+ """Catch U{bug #23187<https://gna.org/bugs/?23187>}, deleting
residue in GUI, and then open spin viewer crashes relax."""
+
+ # Mf tab: Simulate the new analysis wizard.
+ analysis = self.new_analysis_wizard(analysis_type='mf',
analysis_name='Mf test', pipe_name='mf', pipe_bundle='mf bundle')
+
+ self._execute_uf(uf_name='residue.create', res_num=1)
+ self._execute_uf(uf_name='residue.create', res_num=2)
+
+ # Launch the spin viewer window.
+ self.app.gui.show_tree()
+
+ # Close the spin viewer window.
+ self.app.gui.spin_viewer.handler_close()
+
+ # Delete spin,
+ self._execute_uf(uf_name='residue.delete', res_id=":2")
+
+ # Launch the spin viewer window.
+ self.app.gui.show_tree()
+
+
def test_new_analysis_wizard_memory_leak(self):
"""Test for memory leaks in the new analysis wizard."""
Modified: branches/nmrglue/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/relax_disp.py?rev=27166&r1=27165&r2=27166&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/relax_disp.py (original)
+++ branches/nmrglue/test_suite/system_tests/relax_disp.py Wed Jan 14
16:41:27 2015
@@ -1449,6 +1449,78 @@
# Assert that the number of columns is equal, plus 1 for "#".
self.assertEqual(nr_split_header, len(line_split_val) + 1)
+
+
+ def test_bug_23186_cluster_error_calc_dw(self):
+ """Catch U{bug #23186<https://gna.org/bugs/?23186>}: Error
calculation of individual parameter "dw" from Monte-Carlo, is based on first
spin."""
+
+ # Clear the data store.
+ self.interpreter.reset()
+
+ # Load the state.
+ state = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_23186.bz2'
+ self.interpreter.state.load(state, force=True)
+
+ # Dic key to spectrometer frq.
+ dickey = 'SQ CPMG - 599.89086220 MHz'
+
+ # First get the resi 0 array of sim r2a.
+ resi_0_r2a = []
+
+ # Loop over the dics in spin.
+ for cdic in cdp.mol[0].res[0].spin[0].r2a_sim:
+ resi_0_r2a.append(cdic[dickey])
+
+ # Get stats with numpy
+ resi_0_r2a_std = std(asarray(resi_0_r2a), ddof=1)
+
+ # First get the resi 86 array of sim r2a.
+ resi_86_r2a = []
+
+ # Loop over the dics in spin.
+ for cdic in cdp.mol[0].res[1].spin[0].r2a_sim:
+ resi_86_r2a.append(cdic[dickey])
+
+ # Get stats with numpy
+ resi_86_r2a_std = std(asarray(resi_86_r2a), ddof=1)
+
+ # Then get for dw.
+
+ # First get the array of sim dw.
+ resi_0_dw = cdp.mol[0].res[0].spin[0].dw_sim
+ resi_86_dw = cdp.mol[0].res[1].spin[0].dw_sim
+
+ # Get stats with numpy
+ resi_0_dw_std = std(asarray(resi_0_dw), ddof=1)
+ resi_86_dw_std = std(asarray(resi_86_dw), ddof=1)
+
+ # Then get for spin independent parameter.
+
+ # First get the array of sim dw.
+ resi_0_kAB = cdp.mol[0].res[0].spin[0].k_AB_sim
+ resi_86_kAB = cdp.mol[0].res[1].spin[0].k_AB_sim
+
+ # Get stats with numpy
+ resi_0_kAB_std = std(asarray(resi_0_kAB), ddof=1)
+ resi_86_kAB_std = std(asarray(resi_0_kAB), ddof=1)
+
+ # Assume they both std of k_AB values are equal
+ self.assertEqual(resi_0_kAB_std, resi_86_kAB_std)
+
+ # Perform error analysis.
+ self.interpreter.monte_carlo.error_analysis()
+
+ # Check values for k_AB.
+ self.assertEqual(resi_0_kAB_std, cdp.mol[0].res[0].spin[0].k_AB_err)
+ self.assertEqual(resi_86_kAB_std, cdp.mol[0].res[1].spin[0].k_AB_err)
+
+ # Check values for r2a.
+ self.assertEqual(resi_0_r2a_std,
cdp.mol[0].res[0].spin[0].r2a_err[dickey])
+ self.assertEqual(resi_86_r2a_std,
cdp.mol[0].res[1].spin[0].r2a_err[dickey])
+
+ # Check values for dw.
+ self.assertEqual(resi_0_dw_std, cdp.mol[0].res[0].spin[0].dw_err)
+ self.assertEqual(resi_86_dw_std, cdp.mol[0].res[1].spin[0].dw_err)
def test_bug_9999_slow_r1rho_r2eff_error_with_mc(self):
r27166 - in /branches/nmrglue: ./ gui/ specific_analyses/relax_disp/ test_suite/gui_tests/ test_suite/shared_data/dispersion...